#!/bin/bash -e

function info() {
echo Usage: `basename $0` in.vcf
exit 65
}

while getopts  ":i:p:" opts
do
        case  $opts  in
        i) intervals=$OPTARG;;
		p) out_prefix=$OPTARG;;
		*) info;;
        esac
done
shift $(($OPTIND - 1))

if test -z "$1"; then info; fi


. /mnt/ilustre/app/medical/tools/.var



echo;echo;echo VEP annotation no pick '(can not run in background)'
$tools_path/ensembl-tools-release-82/scripts/variant_effect_predictor/variant_effect_predictor.pl \
--offline \
--force_overwrite \
--dir $data_path/ensembl/ \
--fasta $ref_genome \
--refseq \
--hgvs \
--format vcf \
--vcf \
--input_file $1 \
--output_file $out_prefix.vep.vcf

. $cmd_done